A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-09-20, 20:49 UTC
based on data in:
/home/sequser/amrnanopro/work/1e/b3e516dfaeaf198a5c218b3144e717
amrnanopro Software Versions
are collected at run time from the software output.
| Process Name | Software | Version |
|---|---|---|
| CHOPPER | chopper | 0.2.0 |
| CUSTOM_DUMPSOFTWAREVERSIONS | python | 3.11.7 |
| yaml | 5.4.1 | |
| NANOPLOT_AFTER_CHOPPER | nanoplot | 1.41.6 |
| NANOPLOT_BEFORE_CHOPPER | nanoplot | 1.41.6 |
| Workflow | Nextflow | 23.04.4 |
| amrnanopro | 1.0dev |
NanoStat
NanoStat reports various statistics from a long read sequencing dataset in FASTQ, BAM or sequencing summary format.DOI: 10.1093/bioinformatics/bty149.
Summary Statistics
| Sample Name | Median length | Read N50 | Median Qual | # Reads (K) | Total Bases (Mb) |
|---|---|---|---|---|---|
| after_chopperNanoStats | 1079bp | 6184bp | 15.4 | 15.3K | 39.4Mb |
| before_chopperNanoStats | 1062bp | 6204bp | 15.3 | 15.7K | 40.1Mb |
Reads by quality
Read counts categorised by read quality (Phred score).
Sequencing machines assign each generated read a quality score using the Phred scale. The phred score represents the liklelyhood that a given read contains errors. High quality reads have a high score.